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Yorodumi- PDB-3vlm: Crystal Structure Analysis of the Met244Ala Variant of KatG from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vlm | ||||||
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Title | Crystal Structure Analysis of the Met244Ala Variant of KatG from Haloarcula marismortui | ||||||
Components | Catalase-peroxidase 2 | ||||||
Keywords | OXIDOREDUCTASE / CATALASE-PEROXIDASE | ||||||
Function / homology | Function and homology information catalase-peroxidase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Haloarcula marismortui (Halophile) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Sato, T. / Ten-i, T. / Higuchi, W. / Yoshimatsu, K. / Fujiwara, T. | ||||||
Citation | Journal: To be Published Title: Crystal Structure and Kinetic Studies on Met244Ala Variant of KatG from HALOARCULA MARISMORTUI Authors: Sato, T. / Ten-i, T. / Higuchi, W. / Yoshimatsu, K. / Fujiwara, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vlm.cif.gz | 267.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vlm.ent.gz | 215.6 KB | Display | PDB format |
PDBx/mmJSON format | 3vlm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/3vlm ftp://data.pdbj.org/pub/pdb/validation_reports/vl/3vlm | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 82229.070 Da / Num. of mol.: 2 / Mutation: M244A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haloarcula marismortui (Halophile) / Strain: ATCC 43049 / Gene: katG2 / Production host: Haloferax volcanii (archaea) / References: UniProt: O59651, catalase-peroxidase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.11 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2.67M ammonium sulfate, 0.5M potassium chloride, 20mM sodium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 25, 2006 |
Radiation | Monochromator: conforcal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→35 Å / Num. all: 116127 / Num. obs: 116127 / % possible obs: 93.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.59 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 2.01→2.08 Å / Redundancy: 3.57 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.3 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→24.94 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.867 / SU B: 11.524 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.063 Å2
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Refinement step | Cycle: LAST / Resolution: 2.33→24.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.33→2.391 Å / Total num. of bins used: 20
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